alchemist-incarnation-biochemistry/it.unibo.alchemist.model.biochemistry.environments/BioRect2DEnvironment

BioRect2DEnvironment

open class BioRect2DEnvironment(incarnation: BiochemistryIncarnation, minX: Double, maxX: Double, minY: Double, maxY: Double) : AbstractLimitedContinuous2D<Double> (source)

A rectangular environment for cells, bounded by minX, maxX, minY, and maxY. Inconsistent bounds (a maximum not greater than its minimum) fall back to -1 and 1 for all bounds.

Inheritors

BioRect2DEnvironmentNoOverlap

Constructors

BioRect2DEnvironment

constructor(incarnation: BiochemistryIncarnation, minX: Double, maxX: Double, minY: Double, maxY: Double)

constructor(incarnation: BiochemistryIncarnation)

Builds an unbounded environment.

Properties

currentPosition

open val Node<Double>.currentPosition: Euclidean2DPosition

dimensions

override val dimensions: Int

incarnation

override val incarnation: Incarnation<Double, Euclidean2DPosition>

isTerminated

open override val isTerminated: Boolean

layers

override val layers: Map<Molecule, Layer<Double, Euclidean2DPosition>>

neighborhood

open val Node<Double>.neighborhood: Observable<Neighborhood<Double>>

networkModel

override var networkModel: NetworkModel<Double>

nodeCount

override val nodeCount: Observable<Int>

nodes

open override val nodes: ObservableList<Node<Double>>

offset

override val offset: DoubleArray

origin

open override val origin: Euclidean2DPosition

position

open val Node<Double>.position: Observable<Euclidean2DPosition>

reactions

open override val reactions: ObservableList<Reaction<Double>>

shapeFactory

open override val shapeFactory: Euclidean2DShapeFactory

simulation

override var simulation: Simulation<Double, Euclidean2DPosition>

simulationOrNull

override var simulationOrNull: Simulation<Double, Euclidean2DPosition>?

size

override val size: DoubleArray

sizeInDistanceUnits

open override val sizeInDistanceUnits: DoubleArray

Functions

addLayer

open override fun addLayer(molecule: Molecule, layer: Layer<Double, Euclidean2DPosition>)

addNode

open override fun addNode(node: Node<Double>, position: Euclidean2DPosition): Boolean

addReaction

open override fun addReaction(reaction: Reaction<Double>)

addTerminator

open fun addTerminator(terminator: (Environment<Double, Euclidean2DPosition>) -> Boolean)

open override fun addTerminator(terminator: TerminationPredicate<Double, Euclidean2DPosition>)

contains

open operator override fun contains(node: Node<Double>): Boolean

currentPositionOf

open override fun currentPositionOf(node: Node<Double>): Euclidean2DPosition

distanceBetween

open override fun distanceBetween(n1: Node<Double>, n2: Node<Double>): Double

distanceTo

open fun Node<Double>.distanceTo(other: Node<Double>): Double

farthestReachablePosition

open override fun farthestReachablePosition(node: Node<Double>, desired: Euclidean2DPosition): Euclidean2DPosition

The farthest position reachable by node towards desired, clamped within the limits of this environment.

getHeading

open override fun getHeading(node: Node<Double>): Euclidean2DPosition

getNodesWithin

open override fun getNodesWithin(shape: Euclidean2DShape): List<Node<Double>>

getShape

open override fun getShape(node: Node<Double>): Euclidean2DShape

layerFor

open override fun layerFor(molecule: Molecule): Layer<Double, Euclidean2DPosition>?

makePosition

open fun makePosition(coordinates: DoubleArray): Euclidean2DPosition

open fun makePosition(coordinates: List<Number>): Euclidean2DPosition

open fun makePosition(x: Double, y: Double): Euclidean2DPosition

open fun makePosition(x: Number, y: Number): Euclidean2DPosition

open override fun makePosition(vararg coordinates: Number): Euclidean2DPosition

moveBy

open fun Node<Double>.moveBy(displacement: Euclidean2DPosition)

moveNodeBy

open fun moveNodeBy(node: Node<Double>, displacement: Euclidean2DPosition)

moveNodeTo

open override fun moveNodeTo(node: Node<Double>, position: Euclidean2DPosition)

Only cells move. After a cell moves, its junctions with nodes that are no longer neighbors are removed.

moveTo

open fun Node<Double>.moveTo(position: Euclidean2DPosition)

neighborhoodOf

open override fun neighborhoodOf(node: Node<Double>): Observable<Neighborhood<Double>>

nodesAround

open override fun nodesAround(position: Euclidean2DPosition, range: Double): List<Node<Double>>

open override fun nodesAround(node: Node<Double>, range: Double): List<Node<Double>>

nodesInRange

open fun Euclidean2DPosition.nodesInRange(range: Double): List<Node<Double>>

open fun Node<Double>.nodesInRange(range: Double): List<Node<Double>>

nodeWithId

open override fun nodeWithId(id: Int): Node<Double>

observeLayerValue

open override fun observeLayerValue(molecule: Molecule, node: Node<Double>): Observable<Double?>

observeNodesAround

open override fun observeNodesAround(position: Euclidean2DPosition, range: Double): ObservableSet<Node<Double>>

open override fun observeNodesAround(node: Node<Double>, range: Double): ObservableSet<Node<Double>>

observeNodesInRange

open fun Euclidean2DPosition.observeNodesInRange(range: Double): ObservableSet<Node<Double>>

open fun Node<Double>.observeNodesInRange(range: Double): ObservableSet<Node<Double>>

positionOf

open override fun positionOf(node: Node<Double>): Observable<Euclidean2DPosition>

remove

open fun Node<Double>.remove()

open fun Reaction<Double>.remove()

removeNode

open override fun removeNode(node: Node<Double>)

removeReaction

open override fun removeReaction(reaction: Reaction<Double>)

setHeading

open override fun setHeading(node: Node<Double>, direction: Euclidean2DPosition)

toPosition

open fun DoubleArray.toPosition(): Euclidean2DPosition

toString

open override fun toString(): String